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[protege-discussion] Ontology list won't display

Timothy Redmond tredmond at stanford.edu
Fri Oct 2 14:27:23 PDT 2009



> In the previous email said that the URL
> "http://natsuda.tomcat.debii.curtin.edu.au/"  is alias that are the
> same with "http://localhost:8080/webprotege/" but without state the
> "webprotege" in its path. If I put URL
> "http://natsuda.tomcat.debii.curtin.edu.au/webprotege", the web page
> will look like this
> 
	...
> If I used the URL http://natsuda.tomcat.debii.curtin.edu.au/ , the web
> page appears (please refer to the picture below).

The point is that we don't know how you did this and it seems more and
more likely that this is the crux of the problem that you are having.
We tried several tricks to obtain your configuration and they did not
work.

If natsuda.tomcat.debii.curtin.edu.au is running tomcat using port 80
then we would expect that 

	http://natsuda.tomcat.debii.curtin.edu.au/webprotege

would show the webprotege login.  So either 

     1. the tomcat installation has been modified to show web
        applications differently,
     2. the webprotege installation has been modified to display
        differently, or
     3. tomcat is running on a different host or on a port other than 80
        and some server on natsuda.tomcat.debii.curtin.edu.au is
        connecting to the tomcat installation to provide services on
        port 80. 
 
The latter was actually my guess and it seemed to be what you were
saying in your last message.  So I conjectured that maybe
natsuda.tomcat.debii.curtin.edu.au might be running apache http on port
80 which was somehow talking to tomcat on another port or host.  I
believe that this is what our sysadmin has done to make 

	http://bmir-protege-dev1.stanford.edu/webprotege/

work correctly.  If this was the case then my question would be "what
happens if you access the tomcat host and port directly?"

In any case, we don't know how your machines have been configured.  We
don't know how to replicate it here. It seems quite possible that web
protege is not working there because of something custom that you have
done to your installation.


> From your quote, I don't understand that if the tomcat doesn't expand
> the war file itself, then I am deploying to the wrong place. But how
> come the "WebProtege.html" can display on the browser? 

By default, tomcat automatically notices when a war file is deposited
in the webapps directory.  If it is running when the file appears, it
will automatically undeploy and delete the currently running web
application, expand the war file and then redeploy.

It is of course possible that tomcat has been configured not to do this
(I don't know this setting but such a setting would not surprise me).

-Timothy

On Sat, 2009-10-03 at 02:10 +0800, Natsuda Kasisopha wrote:
> Hi Timothy,
> 
> Thanks for you reply. In the previous email said that the URL
> "http://natsuda.tomcat.debii.curtin.edu.au/"  is alias that are the
> same with "http://localhost:8080/webprotege/" but without state the
> "webprotege" in its path. If I put URL
> "http://natsuda.tomcat.debii.curtin.edu.au/webprotege", the web page
> will look like this
> 
> 
> 
> 
> If I used the URL http://natsuda.tomcat.debii.curtin.edu.au/ , the web
> page appears (please refer to the picture below).
>  
> 
> 
> And if you want the real URL, I have to ask the server administrator
> and get back to you soon. 
> 
> "You should be able to simply upload the war file to the webapps
> directory and tomcat will expand the war file itself.  If this is not
> happening then somehow you are deploying to the wrong place."
> 
> From your quote, I don't understand that if the tomcat doesn't expand
> the war file itself, then I am deploying to the wrong place. But how
> come the "WebProtege.html" can display on the browser? 
> 
> I just try to have the ontology list display with the WebProtege.html
> page. 
> 
> Thanks you,
> Natsuda
> 
> 
> 
> Timothy Redmond wrote: 
> > 
> > > Sorry for the confusion and frustration on my problem. I'm no
> > > different from you. You were talking about the URL of my web site
> > > "http://natsuda.tomcat.debii.curtin.edu.au/" and how did the
> > > "webprotege" didn't appears on the URL, the URL of
> > > "http://natsuda.tomcat.debii.curtin.edu.au/"  is another alias
> > > that equivalence to "http://localhost:8080/webprotege/" but
> > > different host name. 
> > 
> > So this might be the key.  An important question is what happens
> > when you access tomcat directly with 
> > 
> >     http://localhost:8080/webprotege 
> > 
> > on the different host. 
> > 
> > > According to your instruction and the instruction in the wiki, the
> > > Tomcat suppose to unzip the "webprotege.war" automatically but the
> > > winSCP doesn't do that. Thus I unzip the file on my computer and
> > > then upload them to the server. 
> > 
> > You should be able to simply upload the war file to the webapps
> > directory and tomcat will expand the war file itself.  If this is
> > not happening then somehow you are deploying to the wrong place. 
> > 
> > -Timothy 
> > 
> > On Oct 2, 2009, at 5:16 AM, Natsuda Kasisopha wrote: 
> > 
> > > Dear Jennifer, 
> > > 
> > > Sorry for the confusion and frustration on my problem. I'm no
> > > different from you. You were talking about the URL of my web site
> > > "http://natsuda.tomcat.debii.curtin.edu.au/" and how did the
> > > "webprotege" didn't appears on the URL, the URL of
> > > "http://natsuda.tomcat.debii.curtin.edu.au/"  is another alias
> > > that equivalence to "http://localhost:8080/webprotege/" but
> > > different host name. If you put
> > > "http://natsuda.tomcat.debii.curtin.edu.au/webprotege/WebProtege.html", it would appear Error message "HTTP Status 404  - /webprotege/webprotege/WebProtege.html". This has shown that the URL "http://natsuda.tomcat.debii.curtin.edu.au/" already pointing to  "webapps/webprotege/WebProtege.html" just like  "http://localhost:8080/webprotege/" path. 
> > > 
> > > On your request of how am I deployed the Web Protege on the
> > > server. First of all, I'm using a shared server (host) name
> > > "blade1.debii.curtin.edu.au" of the institute that I am studying
> > > at. I access the server remotely by using winSCP. I don't have the
> > > direct access to the server. According to your instruction and the
> > > instruction in the wiki, the Tomcat suppose to unzip the
> > > "webprotege.war" automatically but the winSCP doesn't do that.
> > > Thus I unzip the file on my computer and then upload them to the
> > > server. The directory path on the server, the server administrator
> > > manage and provide for me. I'm only allow to modify/delete the
> > > content in webprotege folder. 
> > > 
> > > I notice in the log file i sent you. There were a fill Warning
> > > about the "plugins" directory, please refer to the message below.
> > > Is this directory need for the Web Protege page? 
> > > WARNING: Plugins directory not
> > > found: /usr/local/tomcat5/webapps/webprotege/plugins 
> > > 30-Sep-2009 13:57:39
> > > edu.stanford.smi.protege.resource.BundleHelper <init> 
> > > 
> > > WARNING: Plugins directory not
> > > found: /usr/local/tomcat5/webapps/webprotege/plugins 
> > > 30-Sep-2009 13:57:39
> > > edu.stanford.smi.protege.resource.BundleHelper <init> 
> > > 
> > > I hope the information I give would help. 
> > > Nat 
> > > 
> > > Jennifer Vendetti wrote: 
> > > > Hello Natsuda, 
> > > > 
> > > > We are trying to reproduce your problem here, but have been
> > > > unsuccessful so far.  One question we have is how you managed to
> > > > configure your server such that there is no "webprotege" in the
> > > > path to the WebProtege application.  In other words, you sent us
> > > > the URL of "http://natsuda.tomcat.debii.curtin.edu.au/", which
> > > > launches WebProtege.  But, if we run WebProtege using the
> > > > standard way of deploying the WAR file to Tomcat, we end up with
> > > > a URL that looks like this: http://localhost:8080/webprotege/.
> > > > One possibility is that the aliases that your admin has set up
> > > > is somehow preventing WebProtege from finding the projects that
> > > > are listed in the metaproject.  But, we are having trouble
> > > > reproducing your particular deployment scenario.  Are there any
> > > > more details you can give us about how you set up your
> > > > deployment - in particular, how did you eliminate the
> > > > "webprotege" portion of the path? 
> > > > 
> > > > Jennifer 
> > > _______________________________________________ 
> > > protege-discussion mailing list 
> > > protege-discussion at lists.stanford.edu 
> > > https://mailman.stanford.edu/mailman/listinfo/protege-discussion 
> > > 
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